Dear Oguz,
You can't get the density / volume information in the md.out file. As
the volume is fixed, you will have to calculate it yourself from the box
dimensions in the coordinate file. Alternatively, do one step of
constant pressure dynamics and then the output file from this will have
the volume and density.
The density (and volume) in a normal constant volume run will not vary,
by definition, so you don't need to calculate it constantly.
On Mon, 2009-02-16 at 16:32 +0200, oguz gurbulak wrote:
> Dear Andrew,
>
> Thank you very much for your attention. But what should I do in my
> md.ininput file to see the density and volume information in md.out
> file.
>
> Kind regards.
>
> MD equilibration
> &cntrl
> imin=0, irest=0, nstlim=10000, dt=0.002, ntx=1,
> ntc=2, ntf=2, ntpr=500, ntwx=500, ntwr=500, ntwe=500, ntwv=500,
> cut=9.825, ntb=1, ntp=0, ntr=0, ntt=1,tautp=2.0, vlimit=5,
> tempi=0.0, temp0=273.0,
> /
>
> 2009/2/16 Andrew Purkiss-Trew <a.purkiss.mail.cryst.bbk.ac.uk>
>
> > This is because the density and volume do not appear in the mdout file
> > and the perl script that processes the file just gives a single column
> > (time) in the relevant processed files. If you look at summary.VOLUME,
> > you will see just the time column, compare this with summary.ETOT where
> > you will see two columns: time and energy.
> >
> > Your graphs just show the result of plotting x vs x and are a 'feature'
> > of xmgrace when there is no y data to plot.
> >
> > On Mon, 2009-02-16 at 15:58 +0200, oguz gurbulak wrote:
> > > Dear All,
> > >
> > > I run a md in NVT ensamble. And I wanted to see the graphs of density and
> > > volume with using xmgrace. I realized that both density and volume
> > increase
> > > at the end of the md. I didn't find what the problem is about my
> > operation.
> > > Could you help me to learn the reason ?
> > >
> > >
> > > MD equilibration
> > > &cntrl
> > > imin=0, irest=0, nstlim=10000, dt=0.002, ntx=1,
> > > ntc=2, ntf=2, ntpr=500, ntwx=500, ntwr=500, ntwe=500, ntwv=500,
> > > cut=9.825, ntb=1, ntp=0, ntr=0, ntt=1,tautp=2.0, vlimit=5,
> > > tempi=0.0, temp0=273.0,
> > > /
> > >
> > >
> > > Thank you very much for your attention.
> > >
> > > Kind regards.
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> >
> >
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Received on Wed Feb 18 2009 - 01:10:12 PST
